All I've Seen Has Changed My Mind
by The Lonely Centurion
Summary: Sorry in advance for the terrible summary: 11th Doctor Amy, & Rory after THE WEDDING OF RIVER SONG , somehow a man appears on the TARDIS. Reborn Doctor Chronicles Book One
1. Chapter 1

_**Disclaimer – Doctor Who is owned by the BBC, this is clearly fan fiction.**_

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><p><span>Chapter 1<span>

The Doctor sat in the chair in the console room of the TARDIS, Amy and Rory were sleeping. Bunk beds he thought to himself sometimes humans don't understand the fun in bunk beds or my sense of humor. The TARDIS beeped and gurgled.

"Well I know you do dear," said the Doctor, "We are psychically connected you know. At least there's a short break from our usual crashing and exploding and whatnot."

Just then the TARDIS lurched forward and all the whirring sounds and lights ceased as everything went to black inside the wondrous machine. "Well it seems like I spoke too soon," said the Doctor.

"Uggh" came a groan as a not to pleasant Rory Williams entered the console room, soon followed by his wife. "Doctor stopping short and sleeping in bunk beds don't really work well."

The Doctor managed to suppress a chuckle, but Amy wasn't able to. She cautiously bit her lip to calm herself down before asking, "Well why have we stopped and why is everything turned off?"

"That's actually a really good question Pond. It's probably some kind of wonky thing with some stuff that has gone horribly wrong that will put us all in danger when I tried to fix it," responded the Doctor.

"Oh so it's Tuesday," Amy said.

"Amelia Pond, how many times do I have to tell you that we're in a time machine? It's not Tuesday, it's not any day in here," responded the Doctor.

"I'm sorry to interrupt your crucial debate over the days of the week," said Rory, "But why don't you look over there."

The Doctor and Amy turned towards the direction that Rory was pointing. At the top of the stairs, glowing particles of yellow dust seemed to swarm through the air making a rough circle shape.

"Well that is interesting!" exclaimed the Doctor as he began to scan the anomaly with his sonic screwdriver. "Apparently it's TARDIS energy which is odd since I haven't seen it manifest itself like this since Rose." The Doctor paused, and began to think.

Suddenly the particles of TARDIS energized dust solidified into a ring. The Doctor shouted, "Everyone get back, something is coming through, something powerful because nothing should be able to get to this place. Nothing in our Universe should be able to do this."

"Already on it Doctor," called Rory from the doorway to the console room where he was standing protectively in front of his wife.

At that moment a boot began to materialize through what was apparently a portal. The boot was followed by the rest of a tall man. He appeared to be in his late fifties, he was wearing a grey beanie and a tattered ashen military uniform. Grey stubble and soot marked his face as did faint scars that seemed as if they were won in battle. As the man fully appeared inside the TARDIS, the portal behind him began to close and the TARDIS began to regain power.

"Not to be rude, but who are you?" the Doctor shouted up to their visitor. The man said nothing, but his cold eyes looked at the Doctor with contempt and envy. The Doctor shouted again as the man grew closer, "I don't like soldiers and you look like a soldier to me, tell me how you got on my TARDIS?"

The man laughed a low hollow laugh that seemed forced as he continued to walk closer to the Doctor. As he walked he said slowly, "I forgot you were the soldier who turned his back on all other soldiers. You abandoned us and gave us false hope for a future we could never see."

"Who are you?" the Doctor said angrily.

The man laughed his forced laugh yet again before saying, "Isn't it obvious Doctor, I've aged. I've fought battles even you wouldn't believe and I did it without a TARDIS and without a sonic screwdriver," the man paused and removed his grey hat.

Atop his head was hair that was unmistakable. It was a brown mop of hair that was peppered with grey, and it was very unruly.

"No it can't be you," said the Doctor.

Amy who had taken the imitative to step out from behind her husband asked in a hushed tone, "Doctor who is he?"

"Another companion," said the elder man and he then notice Rory, "Ah I see you keep two with you now."

"Yes. I do," responded the Doctor drearily.

"As to who I am," the battle hardened soldier continued, "I am one of the last resistance fighters of Earth. Doctor you see we had no chance in my universe. You had interfered; we had interfered with the Cybus Cybermen. We drew unneeded attention to Earth. Soon we had minor problems with the Nestene Consciousness and the Gelth, but soon enough the Daleks arrived. Doctor I had to watch my world burn around me for the second time, and this time there was nothing I could do about it. I couldn't risk my life the ways I had before because I was mortal. It's your fault I exist and I am here to collect on my debt."

"But what about Rose," said the Doctor, "She must have been worth it?"

"Doctor I loved her with all my being and in time she saw that, but she always saw me as a shadow. I was never the mad man she fell in love with," he paused as tears began to form in his eyes, "She was killed in an attack by a Dalek raiding party a few hours ago, but her connection to the TARDIS didn't die. The Bad Wolf has brought me home Doctor, and I intend to embrace my destiny as a Time Lord once again."

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><p><em>Unlike my other stories this will be the only chapter with an author's note. This story was written on Dec. 12 2011 in its entirety; to be honest I didn't even mean to write this story at all. I meant to write some chapters for my other stories, but I had an idea and I couldn't let it slip away. Anyway Read, Enjoy, and Review. Now Allons-y!<em>


	2. Chapter 2

_**Disclaimer – Doctor Who is owned by the BBC, this is clearly fan fiction.**_

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><p><span>Chapter 2<span>

"Doctor explain now," said Amy with a tone of anger that helped to hide her fear of the situation.

"Yeah, I don't really understand either" said Rory with a tone of genuine confusion.

The Doctor turned to look at his companions, but when he tried to speak he was for once speechless. He had no idea what to say or how to explain the situation they were currently in. For one of the first times since meeting Amy and Rory he was truly helpless to the situation they were in.

"Doctor," Amy shouted, "Who is this man?"

The ashen and tattered soldier stepped forward and said, "I think I can explain better than your Doctor."

"Oh really now," said Amy, "Well why don't you?"

"Amy maybe you shouldn't be so rude to the guy who teleported into the TARDIS who probably can kill us," suggested Rory.

The older laughed his hollow laugh again as the Doctor sunk into his chair with his head in his hands. The man said, "I like this one, a companion who actually has common sense. They were so tough to come by during my tenure. What's your name boy?"

Rory looked around frantically and saw his wife who was terrified putting on a brave face and the Doctor sulking in his chair before responding, "I am Rory Williams, The Last Centurion, the guardian of the Pandorica, and I will not allow you to do any damage to this ship or my wife."

"Brilliant speech Roman," said the man, "but I didn't come here to cause any damage. I came here to fix something your Doctor broke." The timeworn ragged and threadbare soldier looked at the Doctor before saying, "I'm going to tell them who I am, who we are and you're not going to interrupt me are you?"

The Doctor barely moved and was silent. With his head still in his hands he said, "Go ahead tell them whatever you like."

"Thank you Doctor," the scruffy man said. "To start with, you know that the Doctor is a Time Lord and that he can regenerate or has he not even told you that yet?"

"We know," said Rory.

"Well in that case I don't have to explain much," responded the man. "I am the Doctor's tenth incarnation in a sense. I was born from the residual energy in his detached hand. The only difference between us is that I am almost human. I still have Time Lord DNA, but I have only one heart and no regenerations. I'm mortal. The Doctor banished me to another universe with a woman he loved, that I loved, because I was the man who never should have been. I've already told you a bit about the Dalek invasion, but you don't understand how bad it really was." The former Doctor paused before continuing. "Roman I sense you have seen much but you have not seen the Dalek war machine in action. On the first day entire cities were destroyed. Not just blown up but completely obliterated. There was nothing left, not even ash. In the weeks that followed, the survivors were led by myself and Rose Tyler, the Bad Wolf. We fought hard for years, we never knew if there were other pockets of resistance still fighting or if we were the only ones left, but we fought. I wasn't about to let the human race go down without a fight, you're a strong group and you would fight to the very last man. Unfortunately it was a war we could not win. We didn't even have the slightest chance. In the final hours we were pinned down in the remnants of Torchwood Base 6, which was located out in the country side beyond Leeds. We had little food and less ammo, but Rose she gave us hope. She told reminded me that I had beaten the Daleks before and I could do it again. For a minute I believe her and then she was hit by a Dalek blast."

"Wow, I can't even begin to understand what you've been through," said Rory, "But you still haven't explained how you got here."

Tears began to stream down the face of The Man Who Never Was, the Doctor's shadow. He looked at Rory and said, "Do you know why Rose Tyler was called the Bad Wolf? She looked into the heart of the TARDIS and absorbed her energy. She became an immensely powerful being for a few short minutes, but not all of that energy left her body. When she died the remaining TARDIS energy ripped a temporary hole in the universes, it allowed me to return home to my TARDIS."


	3. Chapter 3

_**Disclaimer – Doctor Who is owned by the BBC, this is clearly fan fiction.**_

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><p><span>Chapter 3<span>

The Doctor stood up and approached his counterpart. "I know you've been through a lot but you can't stay on the TARDIS and you can't become a Time Lord again. It just isn't possible."

"Why can't he stay?" asked Amy, "Wouldn't having two of you be better?"

The scruffy man who was once the Doctor responded, "There's no way I'll stay with that man, the man who condemned me to this fate. And actually Doctor, Rose came up with a plan before her death to restore my Time Lord powers. She believed as I do if I absorbed the heart of the TARDIS temporarily as she did, I would become a full time lord again. I would be whole for this first time in my existence."

"You can't do that," said the Doctor, "Its suicide. The only reason Rose survive is because we took the energy and died for her. It was the most painful thing I can remember. You can't do this; I'll find you a peaceful home where you can live out the rest of your days."

"I'm sorry, but I would rather die trying than abandon those I left behind. If this works I should be able to return to the other universe and save them. I can begin again," said the other Doctor.

"Stop it," yelled Amy, "this Rose or Bad Wolf or whoever she was wouldn't want you to do this. She would want you to live. Can't you see that?"

"Amy please stop," said Rory. "He's a desperate man and desperate men have nothing to lose. We all have to let him do this, he needs this."

"But he's the Doctor in a way," said Amy, "I don't want to see him die, we just stopped the Doctor from dying. I can't go through that again."

"That's very touching," said both of the Doctors in unison. The two men turned and looked at each other. They were so different, but at the same time they were the same. They shared a past, a woman, and the will to shape and save humanity. They were Earth's silent heroes. They were the men who stood in the background only to be called upon when they were needed and forgotten soon after. One was the Oncoming Storm and the other was the Man Who Never Was, but they were both the same. They were soldiers and they were lovers, they were pacifists who committed genocide, and they were Time Lords. However most importantly they were equals.

The Doctor looked around the console room taking in the faces of those in his presence. He saw Amy with her ginger hair and red nightie with tears streaming down her face, and Rory with his white shirt and black sweatpants and a resolve like steel. His eyes finally came to the other Doctor, a broken down beaten shadow of the man he left behind. But there was a determination like none other behind those eyes, a will to be more than what he was that forced the Doctor to say, "Well let's give it a shot."

"Allons-y!" said the other Doctor as he ran up towards the TARDIS console. "So how are we going to do this? Shouldn't your friends get out of here so they don't get hurt by the TARDIS energy?"

The Doctor laughed roughly, "I forgot how much I would talk when I was happy and yeah, Amy, Rory you should go to the top of the stairs. You should be safe there."

Amy and Rory quickly ran up the flight of stairs as Amy said quietly to her husband, "He still talks a lot when he's happy."

From the top of the stair Amy and Rory looked down upon the scene that was about to unfold. The two Doctors, talking to each other as they worked on opening the TARDIS' center console.


	4. Chapter 4

_**Disclaimer – Doctor Who is owned by the BBC, this is clearly fan fiction.**_

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><p><span>Chapter 4<span>

The two Doctors were taking apart the TARDIS console, removing things like the wibbly lever and the springy button.

"So what regeneration is this?" asked the alternate Doctor.

"It's the eleventh body," responded the Doctor.

"Can I ask how it happened?" said the alternate Doctor.

"It was radiation poisoning, again" said the Doctor with a laugh as he continued to take apart the TARDIS.

The alternate Doctor laughed his hollow laugh before saying, "Radiation, what is with us and getting killed by radiation?"

"No idea," said the Doctor, "but we really have to start avoiding those situations. We only have a few lives left."

"Well," said the alternate Doctor, "If this all goes well I'll actually have a whole new set of regenerations."

"Lucky you, I'd still be careful around nuclear plants if I were you," replied the Doctor.  
>"I will be," the alternate Doctor declared. "Well if you look at that everything is undone, you might want to step back for this part."<br>As the Doctor began to walk up the stairs he turned and looked at his counterpart. He then said, "Doctor, if this doesn't work I just wanted you to know I'm sorry I abandoned you."

The counterpart responded, "You did what you thought was right, I had just killed and entire fleet of Daleks. All I've seen in the other universe has changed my mind about that day. I could have done something else; I could have given them another option before doing what I did. You were right to have abandoned me, I wasn't ready to be a Time Lord at that point, but I am now."

At that moment the alternate Doctor opened the console and stared into the heart of the TARDIS. A swirl of glowing yellow dust surrounded the man and then entered his body through his mouth and nose. "Well that wasn't so bad," said the alternate Doctor as he suddenly began to go into convulsions. He fell to the floor as his body shook uncontrollably.

Amy gasped at the sight of this and Rory rushed forward to go down the stairs to help the Doctor's counterpart who was writhing in pain. Instead the Doctor blocked him on the stairs and pulled him into a hug. He said, "Rory you can't help him, the TARDIS energy would kill you. We just have to wait and see what happens."

"But he's dying," shouted Rory, "You can't let him die!"

"He knew what he was getting into," responded the Doctor, "He knew! And I won't let you through your life away for him, for me. You have your wife and you can't let her lose you again."

"Fine," said Rory with a look of contempt on his face, as he walked back up the stairs to his wife. When he got there he grabbed her and held her in his arms as he whispered, "Amy, everything is going to be okay. The Doctor said he'll be fine."

Amelia Pond looked at her husband in the eyes before saying as tears streamed down her face, "You stupid face. I know you're lying, but thanks for trying to make me feel better."


	5. Chapter 5

_**Disclaimer – Doctor Who is owned by the BBC, this is clearly fan fiction.**_

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><p><span>Chapter 5<span>

The Doctor and his companions watched helplessly as the other universe's Doctor writhed in pain on the floor of the TARDIS. His eyes had rolled up into his head so only the whites could be seen and tears streamed down his face. He was like that for what seemed like hours but could have been only minutes. Then he suddenly stopped and was completely still. A moment later the yellow TARDIS energy flowed out of his mouth and back into the heart of the TARDIS.

The Doctor left Rory with Amy who was crying hysterically on the balcony of the TARDIS console room. He then solemnly walked down the stairs and approached his counterpart. The Doctor then said, "Well old girl, you gave it your best shot to make him whole again."

The TARDIS rumbled in response, and then the Doctor looked at his counterpart again more carefully. He was breathing, barely breathing but still breathing. The Doctor shouted, "Amy! Rory! He's alive, he's still alive!"

It was at that moment the alternate Doctor opened his eyes. He looked around the room and then stood up groggily.

The Doctor asked him, "How are you feeling? Did it work?"

"Well," he said, "It feels like I have two hearts." The alternate Doctor then saw Amy and Rory looking at him from the balcony. He shouted to them, "You two, come down here!"

The two companions ran down the stairs and met the Doctors at the bottom. Amy said "I thought you had died, did it work?"

"Yes Amy it worked," said the alternate Doctor, "I'm one hundred percent Time Lord again and that means it's time to leave."

"But where will you go?" said Rory.

"I don't know," responded the alternate Doctor, "I still have enough TARDIS energy to open a doorway to another universe without a Doctor. In fact I should be getting back to where I came from; they really need a Doctor there."

Just then without saying anything else, the alternate Doctor ran to the top of the TARDIS stairs and drew an oval in the air with his finger. As soon as he was finished, the oval became a portal of TARDIS energy similar to the one he arrived in. He turned and looked at the Doctor and his companions and said, "I'm sorry to run, but there's a universe to save."

"Hang on a second," said the Doctor, "I meant to give you these last time," and with that he threw the other Doctor a Sonic Screwdriver and a piece of coral.

The alternate Doctor caught the objects swiftly and easily and then looked them. "Wow," he said, "I wouldn't be the Doctor without a Sonic Screwdriver and a TARDIS."

The alternate Doctor looked at the Portal he made and saw that it was closing. He then took another look at the TARDIS and her crew before shouting, "Allons-y!" and jumping through the portal.


	6. Epilogue

_**Disclaimer – Doctor Who is owned by the BBC, this is clearly fan fiction.**_

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><p><span>Epilogue<span>

The portal closed as soon as the alternate Doctor was through it. The Doctor and his companions looked at each other and no one was offended when the Doctor told them that they should go back to bed.

The next morning at breakfast everyone was silent. Finally Amy asked, "Doctor, how exactly did all that happen?"

"Well it's pretty simple Amy, it was Tuesday," said the Doctor.

"Alright well despite the fact that you don't believe in Tuesday's on the TARDIS," said Rory, "What do you think happened to the other Doctor?"

"I'm sure he's off roaming the universe in a big blue box by now because you know, he's just like me," said the Doctor, "just another mad man with a blue box."

THE END ©2011

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><p><em>*I lied there is another author's note. See how I used the copyright symbol, yeah I don't have a copyright. <em>BUT I WOULD BE REALLY ANGRY IF MY STORY ENDED UP ELSEWHERE WITHOUT MY EXPRESS PERMISSION_ which I'm more than happy to give if you ask for it and give me credit. Thanks. Hope you enjoyed the story and if you have time and haven't already check out my other stories._


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